diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java
index e37fbb281..0665186c6 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java
@@ -100,6 +100,8 @@ public class CommonSuffixSplitter {
             final SeqVertex suffixVTemplate = commonSuffix(toSplit);
             if ( suffixVTemplate.isEmpty() ) {
                 return false;
+            } else if ( wouldEliminateRefSource(graph, suffixVTemplate, toSplit) ) {
+                return false;
             } else if ( allVerticesAreTheCommonSuffix(suffixVTemplate, toSplit) ) {
                 return false;
             } else {
@@ -141,6 +143,21 @@ public class CommonSuffixSplitter {
         }
     }
 
+    /**
+     * Would factoring out this suffix result in elimating the reference source vertex?
+     * @param graph the graph
+     * @param commonSuffix the common suffix of all toSplits
+     * @param toSplits the list of vertices we're are trying to split
+     * @return true if toSplit contains the reference source and this ref source has all and only the bases of commonSuffix
+     */
+    private boolean wouldEliminateRefSource(final SeqGraph graph, final SeqVertex commonSuffix, final Collection<SeqVertex> toSplits) {
+        for ( final SeqVertex toSplit : toSplits ) {
+            if ( graph.isRefSource(toSplit) )
+                return toSplit.length() == commonSuffix.length();
+        }
+        return false;
+    }
+
 //    private static int counter = 0;
 
     /**
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
index 57d8aa92c..17f04971b 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
@@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
 
     @Test
     public void testHaplotypeCallerMultiSampleComplex1() {
-        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "57e13aed8dc483514ac15fb757aee1d1");
+        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "fd51f8c7235eb6547b678093c7a01089");
     }
 
     private void HCTestSymbolicVariants(String bam, String args, String md5) {
@@ -88,12 +88,12 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
     @Test
     public void testHaplotypeCallerMultiSampleGGAComplex() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
-                "d89c8a32e9c54f66e0331382cac86b27");
+                "ed3b577e6f7d68bba6774a62d9df9cd9");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
         HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
-                "89a28d4290523dd55117bc4e44212d73");
+                "a594a28d8053c3e969c39de81a9d03d6");
     }
 }
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index 4e291cb59..500db6ae9 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -96,7 +96,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void testHaplotypeCallerMultiSampleGGA() {
         HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
-                "3e2e4a62c6c60d432fa1ca32aee2635b");
+                "28c3b1f276ec8198801aafe880e40fb6");
     }
 
     @Test
@@ -166,7 +166,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void HCTestStructuralIndels() {
         final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
-        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("ab518ae32535714604a4ffc71fe42511"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("cac0d88fa4471c7a0ac96533a9a6354b"));
         executeTest("HCTestStructuralIndels: ", spec);
     }